I was just wondering if anyone could point me in the right direction to learn how to do this. I have seen it mentioned several times but can not find a really good guide. Spring is coming and I want to get some close up shots of flowers and maybe some bugs but I only have a Canon 500d closeup lens to work with right now.

There are really no macro lenses for a nikon camera under $400 are there?

I shoot Canon but I would venture to guess that Nikon is similar. To answer your question about lenses. No. As to stacking, I use Zerene Stacker. You can get a free 30 day trial and download online. Its very user friendly. Just take several shots of your subject (really needs to be static)(use a tripod and remote shutter release) then import them into the program and tell it to Align and Stack. Out pops your finished image. I have stacked as many as 50 or so images with good results and have seen others use many more. This is the simple version, but the program has excellent online help. Give it a try.

As for your question about a good macro lens, I would suggest the Nikon AF Nikkor 28-105mm f/3.5-4.5. I have been using it for about 4 months now and I think it's a very good lens. Here's a good in-depth review of the lens. Nikon's AF Zoom Nikkor 28-105mm f/3.5~4.5D IF MACRO wide-telephoto zoom lens The one bad thing about the lens is that if your camera doesn't have a built in focus drive (I think that's what it's called), then the lens must be manual focused. I know that D40s and D60s don't have one, but I think there are others that don't as well. All in all, I would highly recommend the lens.

There are really no macro lenses for a nikon camera under $400 are there?

Thanks!

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If you're patient, you can find a used 105D 2.8 for sale for around $400. I found mine from craiglist for $450. Fantastic lens. Although it won't focus on your D40, most of macro work is done in manual focus anyways. Plus, even on a D80 and higher which CAN focus this lens, I'd rather focus manually anyways because the motor in the camera is not accurate enough (IMO) to fine tune a focus so close.

As for macro lenses if you are pushed you could consider the Nikon 60mm macro, Tamron 60mm macro or the Sigma 70mm macro. Though a little short for the "ideal" insect lens they are certainly up to the task of producing good macro images. The Sigma and (I think but am not certain) the Nikon are also fullframe compatable whilst the Tamron is crop sensor only.
I certainly have a use for my sigma 70mm macro but I would also say that a good 100mmish (90mm Tamron at the shortest) or longer might be the more ideal for many in insect work.

Honestly both are very similar what they offer. I doubt you would notice a massive difference in working distance between either lens - image quality should be very similar also. Both are going to extend as you focus as well.

AF on both is also not USM/HSM so I would expect similar levels of AF performance, though I've never used either to know if there are any differences in this aspect.